MolNFT v1 · #189898 · protein
The complex structure of LARG1-adpr from legionella pneumophila
7W3S · Type IV secretion protein dot: “The complex structure of LARG1-adpr from legionella pneumophila”. X-ray diffraction, 1 ligand (AR6), 20 pockets (best druggability 0.90). MolNFT v1 #189898 on GenesisL1: 3D structure, binding sites…
- PDB
- 7W3S
- Type
- protein
- Length
- 1,648 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type IV secretion protein dot
- UniProt
- A0A2S6F197
- Ligands
- AR6
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Type IV secretion protein dot | protein | 413 | 34% helix, 23% strand | A0A2S6F197 |
| C | Type IV secretion protein dot | protein | 412 | 32% helix, 22% strand | A0A2S6F197 |
| D | Type IV secretion protein dot | protein | 410 | 32% helix, 23% strand | A0A2S6F197 |
Ligands and binding sites
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.90 | 0.93 | 99 | AR6 |
| 2 | 753 | 0.80 | 0.83 | 94 | AR6 |
| 3 | 184 | 0.79 | 0.94 | 30 | empty |
| 4 | 222 | 0.78 | 0.91 | 53 | AR6 |
| 5 | 62 | 0.74 | 0.99 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1057 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 882 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 809 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 7W3S · The complex structure of Larg1-ADPr from Legionella pneumophila · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A2S6F197
- Elsewhere: RCSB PDB 7W3S · PDBe 7W3S · UniProt A0A2S6F197
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